@genome-spy/core 0.78.0 → 0.79.1

package/dist/bundle/esm-BwiDsqSb.js

@@ -0,0 +1,1367 @@
+import { n as e, r as t } from "./esm-Cx-EbkOj.js";
+import { t as n } from "./esm-VvpZ9hsq.js";
+import { r, t as i } from "./browser-CETrb2cm.js";
+//#region ../../node_modules/@gmod/bam/esm/chunk.js
+var a = class {
+	minv;
+	maxv;
+	bin;
+	endPosition;
+	constructor(e, t, n, r = t.blockPosition + 65536) {
+		this.minv = e, this.maxv = t, this.bin = n, this.endPosition = r;
+	}
+	toString() {
+		return `${this.minv.toString()}..${this.maxv.toString()} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
+	}
+	compareTo(e) {
+		return this.minv.compareTo(e.minv) || this.maxv.compareTo(e.maxv) || this.bin - e.bin;
+	}
+	fetchedSize() {
+		return this.endPosition - this.minv.blockPosition;
+	}
+}, o = 65536, s = o * o;
+function c(e, t = 0) {
+	let n = e[t] | e[t + 1] << 8 | e[t + 2] << 16 | e[t + 3] << 24;
+	return ((e[t + 4] | e[t + 5] << 8 | e[t + 6] << 16 | e[t + 7] << 24) >>> 0) * s + (n >>> 0);
+}
+//#endregion
+//#region ../../node_modules/@gmod/bam/esm/util.js
+function l(e, t) {
+	let n = e.length;
+	if (n === 0) return e;
+	let r;
+	if (t) {
+		let i = t.blockPosition, a = t.dataPosition;
+		r = [];
+		for (let t = 0; t < n; t++) {
+			let n = e[t], o = n.maxv;
+			(o.blockPosition - i || o.dataPosition - a) > 0 && r.push(n);
+		}
+		if (r.length === 0) return r;
+	} else r = e;
+	r.sort((e, t) => {
+		let n = e.minv.blockPosition - t.minv.blockPosition;
+		return n === 0 ? e.minv.dataPosition - t.minv.dataPosition : n;
+	});
+	let i = [r[0]], o = r[0].minv.blockPosition, s = r[0].maxv.blockPosition;
+	for (let e = 1; e < r.length; e++) {
+		let t = r[e], n = t.minv.blockPosition, c = t.maxv.blockPosition;
+		if (n - s < 65e3 && c - o < 5e6) {
+			let e = i[i.length - 1];
+			(c - s || t.maxv.dataPosition - e.maxv.dataPosition) > 0 && (i[i.length - 1] = new a(e.minv, t.maxv, e.bin, t.endPosition), s = c);
+		} else i.push(t), o = n, s = c;
+	}
+	return i;
+}
+function u(e, t) {
+	return { lineCount: c(e, t) };
+}
+function d(e, t = []) {
+	let n = [...t];
+	for (let t of e) n.push(t.minv.blockPosition, t.maxv.blockPosition);
+	n.sort((e, t) => e - t);
+	for (let t of e) {
+		let e = t.maxv.blockPosition, r = 0, i = n.length;
+		for (; r < i;) {
+			let t = r + i >>> 1;
+			n[t] > e ? i = t : r = t + 1;
+		}
+		r < n.length && (t.endPosition = Math.min(t.endPosition, n[r]));
+	}
+}
+function f(e, t, n) {
+	if (t + 4 > e.length) return;
+	let r = new DataView(e.buffer), i = r.getInt32(t, !0), a = {}, o = [], s = new TextDecoder("utf8"), c = t + 4;
+	for (let t = 0; t < i; t++) {
+		if (c + 8 > e.length) return;
+		let i = r.getInt32(c, !0);
+		if (c + 8 + i > e.length) return;
+		let l = n(s.decode(e.subarray(c + 4, c + 4 + i - 1))), u = r.getInt32(c + i + 4, !0);
+		a[l] = t, o.push({
+			refName: l,
+			length: u
+		}), c += 8 + i;
+	}
+	return {
+		chrToIndex: a,
+		indexToChr: o
+	};
+}
+function p(e, t) {
+	return e ? e.compareTo(t) > 0 ? t : e : t;
+}
+function m(e, t = (e) => e) {
+	let n = new TextDecoder(), r = 0, i = 0, a = [], o = {};
+	for (let s = 0; s < e.length; s++) if (!e[s]) {
+		if (i < s) {
+			let c = t(n.decode(e.subarray(i, s)));
+			a[r] = c, o[c] = r;
+		}
+		i = s + 1, r++;
+	}
+	return {
+		refNameToId: o,
+		refIdToName: a
+	};
+}
+function h(e) {
+	let t = 0;
+	for (let n of e) t += n.length;
+	let n = new Uint8Array(t), r = 0;
+	for (let t of e) n.set(t, r), r += t.length;
+	return n;
+}
+function g(e, t, n) {
+	return (e & t) !== t || (e & n) !== 0;
+}
+function _(e, t) {
+	return t === "*" ? e === void 0 : `${e}` != `${t}`;
+}
+function v(e) {
+	if (!e) return "";
+	let { flagInclude: t = 0, flagExclude: n = 0, tagFilter: r } = e;
+	return `:f${t}x${n}${r ? `:${r.tag}=${r.value ?? "*"}` : ""}`;
+}
+function y(e, t) {
+	let { flagInclude: n = 0, flagExclude: r = 0, tagFilter: i } = t, a = [];
+	for (let t = 0, o = e.length; t < o; t++) {
+		let o = e[t];
+		!g(o.flags, n, r) && !(i && _(o.tags[i.tag], i.value)) && a.push(o);
+	}
+	return a;
+}
+function b(e, t, n, r, i = []) {
+	for (let a = 0, o = e.length; a < o; a++) {
+		let o = e[a];
+		if (o.ref_id === t) {
+			if (o.start >= r) break;
+			o.end >= n && i.push(o);
+		} else if (o.ref_id > t) break;
+	}
+	return i;
+}
+//#endregion
+//#region ../../node_modules/@gmod/bam/esm/indexFile.js
+function x(e, t = 5) {
+	let r = new n({ maxSize: t });
+	return (t) => {
+		if (r.has(t)) return r.get(t);
+		let n = e(t);
+		return n && r.set(t, n), n;
+	};
+}
+var S = class {
+	filehandle;
+	renameRefSeq;
+	setupP;
+	constructor({ filehandle: e, renameRefSeq: t = (e) => e }) {
+		this.filehandle = e, this.renameRefSeq = t;
+	}
+	async blocksForRange(e, t, n, r = {}) {
+		t < 0 && (t = 0);
+		let i = (await this.parse(r)).indices(e);
+		if (!i) return [];
+		let a = this.reg2bins(t, n);
+		if (a.length === 0) return [];
+		let o = [], { binIndex: s } = i;
+		for (let [e, t] of a) for (let n = e; n <= t; n++) {
+			let e = s[n];
+			if (e) for (let t = 0, n = e.length; t < n; t++) o.push(e[t]);
+		}
+		return l(o, this.getLowestChunk(i, t));
+	}
+	parse(e = {}) {
+		return this.setupP ||= this._parse(e).catch((e) => {
+			throw this.setupP = void 0, e;
+		}), this.setupP;
+	}
+	async lineCount(e, t) {
+		return (await this.parse(t)).indices(e)?.stats?.lineCount ?? 0;
+	}
+	async hasRefSeq(e, t) {
+		return !!(await this.parse(t)).indices(e);
+	}
+	async estimatedBytesForRegions(e, t) {
+		let n = l((await Promise.all(e.map((e) => this.blocksForRange(e.refId, e.start, e.end, t)))).flat()), r = 0;
+		for (let e of n) r += e.fetchedSize();
+		return r;
+	}
+}, C = class {
+	blockPosition;
+	dataPosition;
+	constructor(e, t) {
+		this.blockPosition = e, this.dataPosition = t;
+	}
+	toString() {
+		return `${this.blockPosition}:${this.dataPosition}`;
+	}
+	compareTo(e) {
+		return this.blockPosition - e.blockPosition || this.dataPosition - e.dataPosition;
+	}
+};
+function w(e, t = 0, n = !1) {
+	if (n) throw Error("big-endian virtual file offsets not implemented");
+	return new C(e[t + 7] * 1099511627776 + e[t + 6] * 4294967296 + e[t + 5] * 16777216 + e[t + 4] * 65536 + e[t + 3] * 256 + e[t + 2], e[t + 1] << 8 | e[t]);
+}
+//#endregion
+//#region ../../node_modules/@gmod/bam/esm/bai.js
+var ee = 21578050, T = 14, E = 1 << T;
+function te(e, t) {
+	return e - e % t;
+}
+function D(e, t) {
+	return e - e % t + t;
+}
+function O(e, t) {
+	return --t, [
+		[0, 0],
+		[1 + (e >> 26), 1 + (t >> 26)],
+		[9 + (e >> 23), 9 + (t >> 23)],
+		[73 + (e >> 20), 73 + (t >> 20)],
+		[585 + (e >> 17), 585 + (t >> 17)],
+		[4681 + (e >> T), 4681 + (t >> T)]
+	];
+}
+var k = class extends S {
+	async _parse(e) {
+		let t = await this.filehandle.readFile(e), n = new DataView(t.buffer);
+		if (n.getUint32(0, !0) !== ee) throw Error("Not a BAI file");
+		let r = n.getInt32(4, !0), i = 8, o, s = [];
+		for (let e = 0; e < r; e++) {
+			s.push(i);
+			let e = n.getInt32(i, !0);
+			i += 4;
+			for (let t = 0; t < e; t += 1) {
+				let e = n.getUint32(i, !0);
+				if (i += 4, e === 37450) i += 4, i += 32;
+				else if (e > 37450) throw Error("bai index contains too many bins, please use CSI");
+				else {
+					let e = n.getInt32(i, !0);
+					i += 4;
+					for (let t = 0; t < e; t++) i += 8, i += 8;
+				}
+			}
+			let r = n.getInt32(i, !0);
+			i += 4;
+			for (let e = 0; e < r; e++) o = p(o, w(t, i)), i += 8;
+		}
+		function c(e) {
+			let r = s[e];
+			if (r === void 0) return;
+			let i = n.getInt32(r, !0), o;
+			r += 4;
+			let c = {};
+			for (let e = 0; e < i; e += 1) {
+				let e = n.getUint32(r, !0);
+				if (r += 4, e === 37450) r += 4, o = u(t, r + 16), r += 32;
+				else if (e > 37450) throw Error("bai index contains too many bins, please use CSI");
+				else {
+					let i = n.getInt32(r, !0);
+					r += 4;
+					let o = Array(i);
+					for (let n = 0; n < i; n++) {
+						let i = w(t, r);
+						r += 8;
+						let s = w(t, r);
+						r += 8, o[n] = new a(i, s, e);
+					}
+					c[e] = o;
+				}
+			}
+			let l = n.getInt32(r, !0);
+			r += 4;
+			let f = Array(l);
+			for (let e = 0; e < l; e++) f[e] = w(t, r), r += 8;
+			return d(Object.values(c).flat(), f.map((e) => e.blockPosition)), {
+				binIndex: c,
+				linearIndex: f,
+				stats: o
+			};
+		}
+		return {
+			bai: !0,
+			firstDataLine: o,
+			maxBlockSize: 65536,
+			indices: x(c),
+			refCount: r
+		};
+	}
+	async indexCov(e, t, n, r) {
+		let i = E, a = t !== void 0, o = (await this.parse(r)).indices(e);
+		if (!o) return [];
+		let { linearIndex: s, stats: c } = o;
+		if (s.length === 0) return [];
+		let l = n === void 0 ? (s.length - 1) * i : D(n, i), u = t === void 0 ? 0 : te(t, i), d = Array(a ? (l - u) / i : s.length - 1), f = s[s.length - 1].blockPosition;
+		if (l > (s.length - 1) * i) throw Error("query outside of range of linear index");
+		let p = s[u / i].blockPosition;
+		for (let e = u / i, t = 0; e < l / i; e++, t++) d[t] = {
+			score: s[e + 1].blockPosition - p,
+			start: e * i,
+			end: e * i + i
+		}, p = s[e + 1].blockPosition;
+		return d.map((e) => ({
+			...e,
+			score: e.score * (c?.lineCount ?? 0) / f
+		}));
+	}
+	reg2bins(e, t) {
+		return O(e, t);
+	}
+	getLowestChunk(e, t) {
+		let { linearIndex: n } = e, r = n.length;
+		return n[Math.min(t >> T, r - 1)];
+	}
+}, A = [
+	0,
+	1996959894,
+	3993919788,
+	2567524794,
+	124634137,
+	1886057615,
+	3915621685,
+	2657392035,
+	249268274,
+	2044508324,
+	3772115230,
+	2547177864,
+	162941995,
+	2125561021,
+	3887607047,
+	2428444049,
+	498536548,
+	1789927666,
+	4089016648,
+	2227061214,
+	450548861,
+	1843258603,
+	4107580753,
+	2211677639,
+	325883990,
+	1684777152,
+	4251122042,
+	2321926636,
+	335633487,
+	1661365465,
+	4195302755,
+	2366115317,
+	997073096,
+	1281953886,
+	3579855332,
+	2724688242,
+	1006888145,
+	1258607687,
+	3524101629,
+	2768942443,
+	901097722,
+	1119000684,
+	3686517206,
+	2898065728,
+	853044451,
+	1172266101,
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+	3244367275,
+	3060149565,
+	1994146192,
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+	2563907772,
+	4023717930,
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+];
+typeof Int32Array < "u" && (A = new Int32Array(A));
+var j = (e, t) => {
+	let n = t === 0 ? 0 : ~~t ^ -1;
+	for (let t = 0; t < e.length; t++) n = A[(n ^ e[t]) & 255] ^ n >>> 8;
+	return n ^ -1;
+}, M = 21582659, N = 38359875, P = new C(0, 0);
+function F(e, t) {
+	return e * 2 ** t;
+}
+function I(e, t) {
+	return Math.floor(e / 2 ** t);
+}
+var L = class extends S {
+	maxBinNumber = 0;
+	depth = 0;
+	minShift = 0;
+	async indexCov() {
+		return [];
+	}
+	parseAuxData(e, t) {
+		let n = new DataView(e.buffer), r = n.getUint32(t, !0), i = r & 65536 ? "zero-based-half-open" : "1-based-closed", a = [
+			"generic",
+			"SAM",
+			"VCF"
+		][r & 15];
+		if (!a) throw Error(`invalid Tabix preset format flags ${r}`);
+		let o = {
+			ref: n.getInt32(t + 4, !0),
+			start: n.getInt32(t + 8, !0),
+			end: n.getInt32(t + 12, !0)
+		}, s = n.getInt32(t + 16, !0), c = s ? String.fromCharCode(s) : "", l = n.getInt32(t + 20, !0), u = n.getInt32(t + 24, !0);
+		return {
+			columnNumbers: o,
+			coordinateType: i,
+			metaValue: s,
+			metaChar: c,
+			skipLines: l,
+			format: a,
+			formatFlags: r,
+			...m(e.subarray(t + 28, t + 28 + u), this.renameRefSeq)
+		};
+	}
+	async _parse(t) {
+		let n = await e(await this.filehandle.readFile(t)), r = new DataView(n.buffer), i, o = r.getUint32(0, !0);
+		if (o === M) i = 1;
+		else if (o === N) i = 2;
+		else throw Error(`Not a CSI file ${o}`);
+		this.minShift = r.getInt32(4, !0), this.depth = r.getInt32(8, !0), this.maxBinNumber = ((1 << (this.depth + 1) * 3) - 1) / 7;
+		let s = this.maxBinNumber, c = r.getInt32(12, !0), l = c >= 30 ? this.parseAuxData(n, 16) : void 0, f = r.getInt32(16 + c, !0), m = 16 + c + 4, h, g = [];
+		for (let e = 0; e < f; e++) {
+			g.push(m);
+			let e = r.getInt32(m, !0);
+			m += 4;
+			for (let t = 0; t < e; t++) {
+				let e = r.getUint32(m, !0);
+				if (m += 4, e > this.maxBinNumber) m += 44;
+				else {
+					m += 8;
+					let e = r.getInt32(m, !0);
+					m += 4;
+					for (let t = 0; t < e; t += 1) {
+						let e = w(n, m);
+						m += 8, m += 8, h = p(h, e);
+					}
+				}
+			}
+		}
+		function _(e) {
+			let t = g[e];
+			if (t === void 0) return;
+			let i = r.getInt32(t, !0);
+			t += 4;
+			let o = {}, c;
+			for (let e = 0; e < i; e++) {
+				let e = r.getUint32(t, !0);
+				if (t += 4, e > s) c = u(n, t + 28), t += 44;
+				else {
+					t += 8;
+					let i = r.getInt32(t, !0);
+					t += 4;
+					let s = Array(i);
+					for (let r = 0; r < i; r += 1) {
+						let i = w(n, t);
+						t += 8;
+						let o = w(n, t);
+						t += 8, s[r] = new a(i, o, e);
+					}
+					o[e] = s;
+				}
+			}
+			return d(Object.values(o).flat()), {
+				binIndex: o,
+				stats: c
+			};
+		}
+		return {
+			csiVersion: i,
+			firstDataLine: h,
+			indices: x(_),
+			refCount: f,
+			csi: !0,
+			maxBlockSize: 65536,
+			...l
+		};
+	}
+	getLowestChunk() {
+		return P;
+	}
+	reg2bins(e, t) {
+		let n = 2 ** (this.minShift + this.depth * 3);
+		t > n && (t = n), --t;
+		let r = 0, i = 0, a = this.minShift + this.depth * 3, o = [];
+		for (; r <= this.depth; a -= 3, i += F(1, r * 3), r += 1) {
+			let n = i + I(e, a), r = i + I(t, a);
+			if (r - n + o.length > this.maxBinNumber) throw Error(`query ${e}-${t} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`);
+			o.push([n, r]);
+		}
+		return o;
+	}
+}, ne = class {
+	read() {
+		throw Error("never called");
+	}
+	stat() {
+		throw Error("never called");
+	}
+	readFile() {
+		throw Error("never called");
+	}
+	close() {
+		throw Error("never called");
+	}
+}, R = {
+	BAM_FPAIRED: 1,
+	BAM_FPROPER_PAIR: 2,
+	BAM_FUNMAP: 4,
+	BAM_FMUNMAP: 8,
+	BAM_FREVERSE: 16,
+	BAM_FMREVERSE: 32,
+	BAM_FREAD1: 64,
+	BAM_FREAD2: 128,
+	BAM_FSECONDARY: 256,
+	BAM_FQCFAIL: 512,
+	BAM_FDUP: 1024,
+	BAM_FSUPPLEMENTARY: 2048
+}, z = "=ACMGRSVTWYHKDBN".split(""), B = /* @__PURE__ */ "F F .F R .R F .R R .F2F1.F2R1.R2F1.R2R1.F1F2.F1R2.R1F2.R1R2.F2F1.F2R1.R2F1.R2R1.F F .R F .F R .R R .F1F2.R1F2.F1R2.R1R2.F2F1.R2F1.F2R1.R2R1.F1F2.R1F2.F1R2.R1R2".split("."), V = [
+	77,
+	73,
+	68,
+	78,
+	83,
+	72,
+	80,
+	61,
+	88,
+	63,
+	63,
+	63,
+	63,
+	63,
+	63,
+	63
+], H = new TextDecoder(), U = 461;
+function W(e, t, n, r, i) {
+	let a = e.byteOffset + n;
+	switch (r) {
+		case 105: {
+			if (a % 4 == 0) return new Int32Array(e.buffer, a, i);
+			let r = Array(i);
+			for (let e = 0; e < i; e++) r[e] = t.getInt32(n + e * 4, !0);
+			return r;
+		}
+		case 73: {
+			if (a % 4 == 0) return new Uint32Array(e.buffer, a, i);
+			let r = Array(i);
+			for (let e = 0; e < i; e++) r[e] = t.getUint32(n + e * 4, !0);
+			return r;
+		}
+		case 115: {
+			if (a % 2 == 0) return new Int16Array(e.buffer, a, i);
+			let r = Array(i);
+			for (let e = 0; e < i; e++) r[e] = t.getInt16(n + e * 2, !0);
+			return r;
+		}
+		case 83: {
+			if (a % 2 == 0) return new Uint16Array(e.buffer, a, i);
+			let r = Array(i);
+			for (let e = 0; e < i; e++) r[e] = t.getUint16(n + e * 2, !0);
+			return r;
+		}
+		case 99: return new Int8Array(e.buffer, a, i);
+		case 67: return new Uint8Array(e.buffer, a, i);
+		case 102: {
+			if (a % 4 == 0) return new Float32Array(e.buffer, a, i);
+			let r = Array(i);
+			for (let e = 0; e < i; e++) r[e] = t.getFloat32(n + e * 4, !0);
+			return r;
+		}
+		default: return;
+	}
+}
+function G(e, t) {
+	return e === 105 || e === 73 || e === 102 ? t << 2 : e === 115 || e === 83 ? t << 1 : t;
+}
+var K = class {
+	fileOffset;
+	_byteArray;
+	_start;
+	_end;
+	_dataView;
+	_cachedEnd;
+	_cachedTags;
+	_cachedLengthOnRef;
+	_cachedNumericCigar;
+	_cachedNUMERIC_MD;
+	_cachedSeqStart;
+	constructor(e) {
+		this._byteArray = e.bytes.byteArray, this._start = e.bytes.start, this._end = e.bytes.end, this.fileOffset = e.fileOffset, this._dataView = e.dataView;
+	}
+	get byteArray() {
+		return this._byteArray;
+	}
+	get flags() {
+		return this._dataView.getUint16(this._start + 18, !0);
+	}
+	get ref_id() {
+		return this._dataView.getInt32(this._start + 4, !0);
+	}
+	get start() {
+		return this._dataView.getInt32(this._start + 8, !0);
+	}
+	get end() {
+		return this._cachedEnd === void 0 && (this._cachedEnd = this.start + this.length_on_ref), this._cachedEnd;
+	}
+	get mq() {
+		let e = (this.bin_mq_nl & 65280) >> 8;
+		return e === 255 ? void 0 : e;
+	}
+	get score() {
+		return this.mq;
+	}
+	get qual() {
+		let e = this.seq_length;
+		if (e === 0) return null;
+		{
+			let t = this.seqStart + (e + 1 >> 1);
+			return this._byteArray.subarray(t, t + e);
+		}
+	}
+	get strand() {
+		return this.isReverseComplemented() ? -1 : 1;
+	}
+	get b0() {
+		return this._start + 36;
+	}
+	get seqStart() {
+		return this._cachedSeqStart === void 0 && (this._cachedSeqStart = this.b0 + this.read_name_length + this.num_cigar_bytes), this._cachedSeqStart;
+	}
+	get tagsStart() {
+		let e = this.seq_length;
+		return this.seqStart + (e + 1 >> 1) + e;
+	}
+	get name() {
+		let e = this.read_name_length - 1, t = this.b0, n = this._byteArray, r = Array(e);
+		for (let i = 0; i < e; i++) r[i] = n[t + i];
+		return String.fromCharCode(...r);
+	}
+	get NUMERIC_MD() {
+		if (this._cachedNUMERIC_MD === void 0) {
+			let e = this.getTagRaw("MD");
+			this._cachedNUMERIC_MD = e instanceof Uint8Array ? e : null;
+		}
+		return this._cachedNUMERIC_MD === null ? void 0 : this._cachedNUMERIC_MD;
+	}
+	get tags() {
+		return this._cachedTags === void 0 && (this._cachedTags = this._computeTags()), this._cachedTags;
+	}
+	getTag(e) {
+		return this._cachedTags === void 0 ? this._findTag(e, !1) : this._cachedTags[e];
+	}
+	getTagRaw(e) {
+		return this._findTag(e, !0);
+	}
+	_findTag(e, t) {
+		let n = e.charCodeAt(0), r = e.charCodeAt(1), i = this.tagsStart, a = this._end, o = this._byteArray;
+		for (; i < a;) {
+			let e = o[i], s = o[i + 1], c = o[i + 2];
+			i += 3;
+			let l = e === n && s === r;
+			switch (c) {
+				case 65:
+					if (l) return String.fromCharCode(o[i]);
+					i += 1;
+					break;
+				case 105:
+					if (l) return this._dataView.getInt32(i, !0);
+					i += 4;
+					break;
+				case 73:
+					if (l) return this._dataView.getUint32(i, !0);
+					i += 4;
+					break;
+				case 99:
+					if (l) return this._dataView.getInt8(i);
+					i += 1;
+					break;
+				case 67:
+					if (l) return this._dataView.getUint8(i);
+					i += 1;
+					break;
+				case 115:
+					if (l) return this._dataView.getInt16(i, !0);
+					i += 2;
+					break;
+				case 83:
+					if (l) return this._dataView.getUint16(i, !0);
+					i += 2;
+					break;
+				case 102:
+					if (l) return this._dataView.getFloat32(i, !0);
+					i += 4;
+					break;
+				case 90:
+				case 72: {
+					let e = i;
+					for (; i < a && o[i] !== 0;) i++;
+					if (l) return t ? o.subarray(e, i) : H.decode(o.subarray(e, i));
+					i++;
+					break;
+				}
+				case 66: {
+					let e = o[i++], t = this._dataView.getInt32(i, !0);
+					if (i += 4, l) return W(o, this._dataView, i, e, t);
+					i += G(e, t);
+					break;
+				}
+				default:
+					c !== void 0 && console.error("Unknown BAM tag type", c);
+					break;
+			}
+		}
+	}
+	_computeTags() {
+		let e = this.tagsStart, t = this._end, n = this._byteArray, r = {};
+		for (; e < t;) {
+			let i = String.fromCharCode(n[e], n[e + 1]), a = n[e + 2];
+			switch (e += 3, a) {
+				case 65:
+					r[i] = String.fromCharCode(n[e]), e += 1;
+					break;
+				case 105:
+					r[i] = this._dataView.getInt32(e, !0), e += 4;
+					break;
+				case 73:
+					r[i] = this._dataView.getUint32(e, !0), e += 4;
+					break;
+				case 99:
+					r[i] = this._dataView.getInt8(e), e += 1;
+					break;
+				case 67:
+					r[i] = this._dataView.getUint8(e), e += 1;
+					break;
+				case 115:
+					r[i] = this._dataView.getInt16(e, !0), e += 2;
+					break;
+				case 83:
+					r[i] = this._dataView.getUint16(e, !0), e += 2;
+					break;
+				case 102:
+					r[i] = this._dataView.getFloat32(e, !0), e += 4;
+					break;
+				case 90:
+				case 72: {
+					let a = e;
+					for (; e < t && n[e] !== 0;) e++;
+					r[i] = H.decode(n.subarray(a, e)), e++;
+					break;
+				}
+				case 66: {
+					let t = n[e++], a = this._dataView.getInt32(e, !0);
+					e += 4, r[i] = W(n, this._dataView, e, t, a), e += G(t, a);
+					break;
+				}
+				default:
+					console.error("Unknown BAM tag type", a);
+					break;
+			}
+		}
+		return r;
+	}
+	isPaired() {
+		return !!(this.flags & R.BAM_FPAIRED);
+	}
+	isProperlyPaired() {
+		return !!(this.flags & R.BAM_FPROPER_PAIR);
+	}
+	isSegmentUnmapped() {
+		return !!(this.flags & R.BAM_FUNMAP);
+	}
+	isMateUnmapped() {
+		return !!(this.flags & R.BAM_FMUNMAP);
+	}
+	isReverseComplemented() {
+		return !!(this.flags & R.BAM_FREVERSE);
+	}
+	isMateReverseComplemented() {
+		return !!(this.flags & R.BAM_FMREVERSE);
+	}
+	isRead1() {
+		return !!(this.flags & R.BAM_FREAD1);
+	}
+	isRead2() {
+		return !!(this.flags & R.BAM_FREAD2);
+	}
+	isSecondary() {
+		return !!(this.flags & R.BAM_FSECONDARY);
+	}
+	isFailedQc() {
+		return !!(this.flags & R.BAM_FQCFAIL);
+	}
+	isDuplicate() {
+		return !!(this.flags & R.BAM_FDUP);
+	}
+	isSupplementary() {
+		return !!(this.flags & R.BAM_FSUPPLEMENTARY);
+	}
+	_isCGTagPattern(e, t) {
+		if (t === 2) {
+			let t = this._dataView.getInt32(e, !0);
+			return (t & 15) == 4 && t >> 4 === this.seq_length;
+		} else return !1;
+	}
+	_computeLengthOnRef() {
+		let e = this._dataView.getInt32(this._start + 16, !0);
+		if (e & R.BAM_FUNMAP << 16) return 0;
+		let t = e & 65535, n = this.b0 + this.read_name_length;
+		if (this._isCGTagPattern(n, t)) {
+			let e = this._dataView.getInt32(n + 4, !0);
+			return (e & 15) != 3 && console.warn("CG tag with no N tag"), e >> 4;
+		}
+		let r = this._byteArray.byteOffset + n;
+		if (r % 4 == 0 && t > 50) {
+			let e = new Uint32Array(this._byteArray.buffer, r, t);
+			this._cachedNumericCigar = e;
+			let n = 0;
+			for (let r = 0; r < t; ++r) {
+				let t = e[r];
+				n += (t >> 4) * (U >> (t & 15) & 1);
+			}
+			return n;
+		}
+		let i = 0;
+		for (let e = 0; e < t; ++e) {
+			let t = this._dataView.getInt32(n + e * 4, !0);
+			i += (t >> 4) * (U >> (t & 15) & 1);
+		}
+		return i;
+	}
+	_computeNumericCigar() {
+		let e = this._dataView.getInt32(this._start + 16, !0);
+		if (e & R.BAM_FUNMAP << 16) return /* @__PURE__ */ new Uint32Array();
+		let t = e & 65535, n = this.b0 + this.read_name_length;
+		if (this._isCGTagPattern(n, t)) return this.tags.CG ?? /* @__PURE__ */ new Uint32Array();
+		let r = this._byteArray.byteOffset + n;
+		if (r % 4 == 0 && t > 50) return new Uint32Array(this._byteArray.buffer, r, t);
+		let i = Array(t);
+		for (let e = 0; e < t; ++e) i[e] = this._dataView.getInt32(n + e * 4, !0) | 0;
+		return i;
+	}
+	get length_on_ref() {
+		return this._cachedLengthOnRef === void 0 && (this._cachedLengthOnRef = this._computeLengthOnRef()), this._cachedLengthOnRef;
+	}
+	get NUMERIC_CIGAR() {
+		return this._cachedNumericCigar === void 0 && (this._cachedNumericCigar = this._computeNumericCigar()), this._cachedNumericCigar;
+	}
+	get CIGAR() {
+		let e = this.NUMERIC_CIGAR, t = "";
+		for (let n = 0, r = e.length; n < r; n++) {
+			let r = e[n], i = r >> 4, a = V[r & 15];
+			t += i + String.fromCharCode(a);
+		}
+		return t;
+	}
+	get num_cigar_ops() {
+		return this.flag_nc & 65535;
+	}
+	get num_cigar_bytes() {
+		return this.num_cigar_ops << 2;
+	}
+	get read_name_length() {
+		return this.bin_mq_nl & 255;
+	}
+	get num_seq_bytes() {
+		return this.seq_length + 1 >> 1;
+	}
+	get NUMERIC_SEQ() {
+		let e = this.seqStart;
+		return this._byteArray.subarray(e, e + this.num_seq_bytes);
+	}
+	get seq() {
+		let e = this.seq_length, t = this.seqStart, n = this._byteArray, r = Array(e), i = 0, a = e >> 1;
+		for (let e = 0; e < a; ++e) {
+			let a = n[t + e];
+			r[i++] = z[(a & 240) >> 4], r[i++] = z[a & 15];
+		}
+		return i < e && (r[i] = z[(n[t + a] & 240) >> 4]), r.join("");
+	}
+	get pair_orientation() {
+		let e = this.flags;
+		if (!(e & 12 || this.ref_id !== this.next_refid)) return B[e >> 4 & 15 | (this.template_length > 0 ? 16 : 0)];
+	}
+	get bin_mq_nl() {
+		return this._dataView.getInt32(this._start + 12, !0);
+	}
+	get flag_nc() {
+		return this._dataView.getInt32(this._start + 16, !0);
+	}
+	get seq_length() {
+		return this._dataView.getInt32(this._start + 20, !0);
+	}
+	get next_refid() {
+		return this._dataView.getInt32(this._start + 24, !0);
+	}
+	get next_pos() {
+		return this._dataView.getInt32(this._start + 28, !0);
+	}
+	get template_length() {
+		return this._dataView.getInt32(this._start + 32, !0);
+	}
+	seqAt(e) {
+		if (e < this.seq_length) {
+			let t = this._byteArray[this.seqStart + (e >> 1)];
+			return e % 2 == 0 ? z[(t & 240) >> 4] : z[t & 15];
+		} else return;
+	}
+	toJSON() {
+		return {
+			fileOffset: this.fileOffset,
+			ref_id: this.ref_id,
+			start: this.start,
+			end: this.end,
+			name: this.name,
+			flags: this.flags,
+			mq: this.mq,
+			CIGAR: this.CIGAR,
+			seq: this.seq,
+			next_refid: this.next_refid,
+			next_pos: this.next_pos,
+			template_length: this.template_length,
+			tags: this.tags
+		};
+	}
+};
+//#endregion
+//#region ../../node_modules/@gmod/bam/esm/sam.js
+function q(e) {
+	let t = e.split(/\r?\n/), n = [];
+	for (let e of t) {
+		let [t, ...r] = e.split(/\t/);
+		t && n.push({
+			tag: t.slice(1),
+			data: r.map((e) => {
+				let t = e.indexOf(":");
+				return {
+					tag: e.slice(0, t),
+					value: e.slice(t + 1)
+				};
+			})
+		});
+	}
+	return n;
+}
+var J = 65536;
+function Y(e, t, n) {
+	return e ?? (t ? new i(t) : n ? new r(n) : void 0);
+}
+function X(e, t) {
+	let { minv: n, maxv: r } = e;
+	return `${n.blockPosition}:${n.dataPosition}-${r.blockPosition}:${r.dataPosition}${v(t)}`;
+}
+var Z = class {
+	renameRefSeq;
+	bam;
+	header;
+	chrToIndex;
+	indexToChr;
+	index;
+	htsget = !1;
+	headerP;
+	chunkFeatureCache = new n({ maxSize: 100 });
+	RecordClass;
+	constructor({ bamFilehandle: e, bamPath: t, bamUrl: n, baiPath: r, baiFilehandle: i, baiUrl: a, csiPath: o, csiFilehandle: s, csiUrl: c, htsget: l, renameRefSeqs: u = (e) => e, recordClass: d }) {
+		this.renameRefSeq = u, this.RecordClass = d ?? K;
+		let f = Y(e, t, n);
+		if (f) this.bam = f;
+		else if (l) this.htsget = !0, this.bam = new ne();
+		else throw Error("no bam source: pass bamFilehandle, bamPath, bamUrl, or htsget: true");
+		let p = Y(s, o, c), m = Y(i, r, a) ?? Y(void 0, t ? `${t}.bai` : void 0, n ? `${n}.bai` : void 0);
+		if (p) this.index = new L({ filehandle: p });
+		else if (m) this.index = new k({ filehandle: m });
+		else if (!l) throw Error("no index source: pass csi*/bai* options or a bamPath/bamUrl so the .bai sibling can be inferred");
+	}
+	async getHeaderPre(t = {}) {
+		if (!this.index) return;
+		let n = await this.index.parse(t), r = n.firstDataLine === void 0 ? void 0 : n.firstDataLine.blockPosition + J, i = await e(r === void 0 ? await this.bam.readFile() : await this.bam.read(r, 0)), a = new DataView(i.buffer);
+		if (a.getInt32(0, !0) !== 21840194) throw Error("Not a BAM file");
+		let o = a.getInt32(4, !0);
+		this.header = new TextDecoder("utf8").decode(i.subarray(8, 8 + o));
+		let s = o + 8, c = f(i, s, this.renameRefSeq);
+		if (c ||= (i = await e(await this.bam.readFile()), f(i, s, this.renameRefSeq)), !c) throw Error("Insufficient data for reference sequences");
+		return this.chrToIndex = c.chrToIndex, this.indexToChr = c.indexToChr, q(this.header);
+	}
+	getHeader(e) {
+		return this.headerP ||= this.getHeaderPre(e).catch((e) => {
+			throw this.headerP = void 0, e;
+		}), this.headerP;
+	}
+	async getHeaderText(e = {}) {
+		return await this.getHeader(e), this.header;
+	}
+	async getSeqId(e, t) {
+		return await this.getHeader(t), this.chrToIndex?.[e];
+	}
+	async getRecordsForRange(e, t, n, r) {
+		let i = await this.getSeqId(e, r);
+		if (i === void 0 || !this.index) return [];
+		let a = await this.index.blocksForRange(i, t - 1, n, r);
+		return this._fetchChunkFeaturesDirect(a, i, t, n, r);
+	}
+	evictOverlappingChunks(e, t) {
+		for (let [n, r] of this.chunkFeatureCache) e <= r.maxBlock && t >= r.minBlock && this.chunkFeatureCache.delete(n);
+	}
+	async _fetchChunkFeaturesDirect(e, t, n, r, i = {}) {
+		let { viewAsPairs: a, filterBy: o, onProgress: s } = i, c = [], l = 0;
+		for (let t = 0, n = e.length; t < n; t++) l += e[t].fetchedSize();
+		let u = 0;
+		s?.(0, l);
+		for (let a = 0, d = e.length; a < d; a++) {
+			let d = e[a], f = X(d, o), p = d.minv.blockPosition, m = d.maxv.blockPosition, h, g = this.chunkFeatureCache.get(f);
+			if (g) h = g.features;
+			else {
+				this.evictOverlappingChunks(p, m);
+				let e = await this._readChunkFeatures(d, i);
+				h = o ? y(e, o) : e, this.chunkFeatureCache.set(f, {
+					minBlock: p,
+					maxBlock: m,
+					features: h
+				});
+			}
+			u += d.fetchedSize(), s?.(u, l), b(h, t, n, r, c);
+		}
+		if (a) {
+			let e = await this.fetchPairs(t, c, i);
+			for (let t = 0, n = e.length; t < n; t++) c.push(e[t]);
+		}
+		return c;
+	}
+	async fetchPairs(e, t, n) {
+		let { pairAcrossChr: r, maxInsertSize: i = 2e5 } = n, a = {}, o = /* @__PURE__ */ new Set();
+		for (let e = 0, n = t.length; e < n; e++) {
+			let n = t[e], r = n.name;
+			a[r] = (a[r] ?? 0) + 1, o.add(n.fileOffset);
+		}
+		let s = [];
+		for (let o = 0, c = t.length; o < c; o++) {
+			let c = t[o], l = c.name;
+			this.index && a[l] === 1 && (r || c.next_refid === e && Math.abs(c.start - c.next_pos) < i) && s.push(this.index.blocksForRange(c.next_refid, c.next_pos, c.next_pos + 1, n));
+		}
+		let c = /* @__PURE__ */ new Map(), l = await Promise.all(s);
+		for (let e = 0, t = l.length; e < t; e++) {
+			let t = l[e];
+			for (let e = 0, n = t.length; e < n; e++) {
+				let n = t[e];
+				c.set(n.toString(), n);
+			}
+		}
+		return (await Promise.all([...c.values()].map(async (e) => {
+			let t = await this._readChunkFeatures(e, n), r = [];
+			for (let e = 0, n = t.length; e < n; e++) {
+				let n = t[e];
+				a[n.name] === 1 && !o.has(n.fileOffset) && r.push(n);
+			}
+			return r;
+		}))).flat();
+	}
+	async _readChunkFeatures(e, n) {
+		let { buffer: r, cpositions: i, dpositions: a } = await t(await this.bam.read(e.fetchedSize(), e.minv.blockPosition, { signal: n.signal }), e);
+		return this.readBamFeatures(r, i, a, e);
+	}
+	async readBamFeatures(e, t, n, r) {
+		let i = 0, a = [], o = 0, s = new DataView(e.buffer), c = n.length > 0, l = t.length > 0;
+		for (; i + 4 < e.length;) {
+			let u = s.getInt32(i, !0), d = i + 4 + u - 1;
+			if (c) {
+				let e = i + r.minv.dataPosition;
+				for (; o < n.length && e >= n[o];) o++;
+			}
+			if (d < e.length) {
+				let c = new this.RecordClass({
+					bytes: {
+						byteArray: e,
+						start: i,
+						end: d
+					},
+					fileOffset: l ? t[o] * 256 + (i - n[o]) + r.minv.dataPosition + 1 : j(e.subarray(i, d)) >>> 0,
+					dataView: s
+				});
+				a.push(c);
+			}
+			i = d + 1;
+		}
+		return a;
+	}
+	async hasRefSeq(e, t) {
+		let n = await this.getSeqId(e, t);
+		return !this.index || n === void 0 ? !1 : this.index.hasRefSeq(n);
+	}
+	async lineCount(e, t) {
+		let n = await this.getSeqId(e, t);
+		return !this.index || n === void 0 ? 0 : this.index.lineCount(n);
+	}
+	async indexCov(e, t, n) {
+		let r = await this.getSeqId(e);
+		return !this.index || r === void 0 ? [] : this.index.indexCov(r, t, n);
+	}
+	async blocksForRange(e, t, n, r) {
+		let i = await this.getSeqId(e, r);
+		return !this.index || i === void 0 ? [] : this.index.blocksForRange(i, t, n, r);
+	}
+	clearFeatureCache() {
+		this.chunkFeatureCache.clear();
+	}
+	async estimatedBytesForRegions(e, t) {
+		if (!this.index) return 0;
+		await this.getHeader(t);
+		let n = e.flatMap((e) => {
+			let t = this.chrToIndex?.[e.refName];
+			return t === void 0 ? [] : [{
+				refId: t,
+				start: e.start,
+				end: e.end
+			}];
+		});
+		return this.index.estimatedBytesForRegions(n, t);
+	}
+};
+//#endregion
+//#region ../../node_modules/@gmod/bam/esm/htsget.js
+async function Q(e, t) {
+	let n = await fetch(e, t);
+	if (!n.ok) throw Error(`HTTP ${n.status} fetching ${e}: ${await n.text()}`);
+	return n;
+}
+async function re({ url: e, headers: t }, n) {
+	let { referer: r, ...i } = t ?? {}, a = e.startsWith("data:") ? await Q(e) : await Q(e, {
+		...n,
+		headers: i
+	});
+	return new Uint8Array(await a.arrayBuffer());
+}
+async function $(t, n) {
+	return h(await Promise.all(t.map(async (t) => e(await re(t, n)))));
+}
+var ie = class extends Z {
+	baseUrl;
+	trackId;
+	constructor(e) {
+		super({
+			htsget: !0,
+			recordClass: e.recordClass
+		}), this.baseUrl = e.baseUrl, this.trackId = e.trackId;
+	}
+	async getRecordsForRange(e, t, n, r) {
+		await this.getHeader(r);
+		let i = `${`${this.baseUrl}/${this.trackId}`}?referenceName=${e}&start=${t}&end=${n}&format=BAM`, o = this.chrToIndex?.[e];
+		if (o === void 0) return [];
+		let s = await $((await (await Q(i, r)).json()).htsget.urls.slice(1), { signal: r?.signal }), c = new C(0, 0);
+		return b(await this.readBamFeatures(s, [], [], new a(c, c, 0)), o, t, n);
+	}
+	async getHeaderPre(e = {}) {
+		let t = await $((await (await Q(`${this.baseUrl}/${this.trackId}?referenceName=na&class=header`, e)).json()).htsget.urls, { signal: e.signal }), n = new DataView(t.buffer);
+		if (n.getInt32(0, !0) !== 21840194) throw Error("Not a BAM file");
+		let r = n.getInt32(4, !0), i = q(new TextDecoder().decode(t.subarray(8, 8 + r))), a = [], o = {}, s = i.filter((e) => e.tag === "SQ");
+		for (let [e, t] of s.entries()) {
+			let n = "", r = 0;
+			for (let e of t.data) e.tag === "SN" ? n = e.value : e.tag === "LN" && (r = +e.value);
+			o[n] = e, a[e] = {
+				refName: n,
+				length: r
+			};
+		}
+		return this.chrToIndex = o, this.indexToChr = a, i;
+	}
+};
+//#endregion
+export { k as BAI, Z as BamFile, K as BamRecord, L as CSI, ie as HtsgetFile };